After the hosts had applied virtually all the pressure without breaking the deadlock - Mark Davies going the closest - it was the Swans who went 1-0 up in the 43rd minute through Luke Moore's deft chip.
But Pratley, who left the Welsh side for Bolton in the summer, squared things by heading home an equaliser in first half stoppage time before Chris Eagles settled the fourth round tie 11 minutes after the break, reacting when Gerhard Tremmel could not hold on to Martin Petrov's strike.
Both teams hit the goalframe after that, Swansea doing so twice, but it was Wanderers who emerged triumphant to progress to the next round.
The result also meant the Trotters - beaten eight times at home this season - have now won three games in a row at their own ground in all competitions.
Bolton boss Owen Coyle, unable to call upon new centre-half Tim Ream, made three changes to his starting line-up from the 3-1 Barclays Premier League victory over Liverpool, bringing Dedryck Boyata and Joe Riley in at the back for Zat Knight and Gretar Steinsson, while in midfield, Pratley replaced Fabrice Muamba.
For the visitors, on-loan midfielder Josh McEachran was handed his first start since arriving from Chelsea as Swans manager Brendan Rodgers completely reshuffled his pack from the 2-0 loss at Sunderland by making 10 adjustments, defender Ashley Williams the only player keeping his place in the team.
Bolton made the first attempt on goal in the sixth minute, Sam Ricketts - another ex-Swansea man - rising in the box to get his head to Eagles' free-kick and Tremmel diving to make the save.
Moments later Eagles turned in the box but made poor contact to scuff his shot well wide, and then saw another effort deflect off target.
In the 19th minute David Ngog found himself one on one with Tremmel but was denied by the feet of the German goalkeeper.
Ngog then tried to line up a volley only to fluff his lines, but Davies showed more potency soon after, cutting inside and firing in a low drive that Tremmel managed to get behind.
The hosts continued to press forward, but conviction was lacking in their finishing once again as Eagles lofted the ball over and Petrov saw a strike saved.
After Mark Gower skied a rare attempt at the other end, Swansea thought they had taken the lead against the run of play when Wayne Routledge tapped in Leroy Lita's cross.
The assistant referee ruled that effort was offside, but then with two minutes of the half remaining, the Swans did find themselves in front as Moore outmuscled David Wheater to clip the ball over Adam Bogdan and into the net.
Bolton managed to hit back before the interval, though, Pratley nodding in Petrov's free-kick to make it 1-1.
It was Pratley's first goal for Wanderers, the last time he netted coming in Swansea's npower Championship play-off semi-final against Nottingham Forest in May.
Seven minutes after the restart Moore collected a pass from McEachran and tried his luck from distance, curling the ball wide.
Swansea were looking more purposeful and Moore almost burst through again, but in the 56th minute Bolton restored their advantage as Tremmel parried Petrov's shot, allowing Eagles to tuck the ball into the corner.
Within seconds, Wanderers survived a scare when Lita hit the woodwork, only for Pratley to then send a header against the Swans' crossbar.
Another chance came Pratley's way as a miscued backpass let him in, but he was unable to get his shot the right side of the post.
Kemy Agustien drove forward for Swansea but could not get his shot on target.
Bolton were soon back on the offensive and either side of a Williams header, Riley and Nigel Reo-Coker fired into the side-netting.
Swans substitute Danny Graham almost salvaged a replay late on, but his header came back off the post and Wanderers' place in round five was confirmed.